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A comprehension of contemporary effort for tracking of lip 对当代唇部追踪研究的理解
Int. J. Bioinform. Res. Appl. Pub Date : 2020-02-02 DOI: 10.1504/ijbra.2020.10026544
M. Nandini, Nagappa U. Bhajantri
{"title":"A comprehension of contemporary effort for tracking of lip","authors":"M. Nandini, Nagappa U. Bhajantri","doi":"10.1504/ijbra.2020.10026544","DOIUrl":"https://doi.org/10.1504/ijbra.2020.10026544","url":null,"abstract":"Lip tracking exercise is the most important pre-requisite for lip reading system. Most of the lip reading procedures are accessible based on lip contour analysis. Similarly, lip contour extraction is a fundamental footstep. As a result of lip contour extraction, initially the process of lip contour detection in the first frame of an audio-visual image sequence. Subsequently capturing contour in successive frames based on methods of automatic, semiautomatic and hybrid is normally named as lip tracking. Here the effort presents an overview of contemporary works on extracting the face from digital video and classified the face into lip area and non-lip area by categorising the approaches into low and high-level processing techniques. Furthermore, the comparative study of approaches and their effectiveness based on various factors like asymmetric lips, the mouth with visible teeth, tongue and mouth with mustache are offered.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123013101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Extrapolating the effect of non-synonymous SNP in bread wheat HSP16.9B gene: a molecular modelling and dynamics study 非同义SNP在面包小麦HSP16.9B基因中的外推效应:分子模型和动力学研究
Int. J. Bioinform. Res. Appl. Pub Date : 2020-02-02 DOI: 10.1504/ijbra.2020.10026545
B. Pandey, Saurabh Gupta, A. Rao, D. M. Pandey, R. Chatrath
{"title":"Extrapolating the effect of non-synonymous SNP in bread wheat HSP16.9B gene: a molecular modelling and dynamics study","authors":"B. Pandey, Saurabh Gupta, A. Rao, D. M. Pandey, R. Chatrath","doi":"10.1504/ijbra.2020.10026545","DOIUrl":"https://doi.org/10.1504/ijbra.2020.10026545","url":null,"abstract":"Small heat shock proteins (sHSP) are molecular chaperons which play a key role in protein homeostasis under stress conditions. Point mutation of aspartic acid (D) substitution for asparagine (N) at residue 11 (D11N) in HSP16.9B protein was predicted in HSP16.9B gene in wheat. However, its impact on protein function and structural consequences has not been explored. In this study, we examined the effect of point mutation using molecular modelling and molecular dynamics (MD) simulations. Moreover, point mutation induced addition of beta-sheet before the mutation position in the mutant protein. Three-dimensional homology protein modelling, structure validation, and molecular dynamics were carried out to investigate the conformational transitions and dynamics of the HSP16.9B protein due to D11N non-synonymous single nucleotide polymorphism (nsSNP). The MD results indicated that the stability of the mutant protein structure during entire simulation runs. Altogether, our investigation will provide useful understanding related to structural and functional basis of HSP16.9.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129289790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In silico deleterious prediction of nonsynonymous single nucleotide polymorphisms in Neurexin1 gene for mental disorders 神经素1基因非同义单核苷酸多态性对精神障碍的计算机有害预测
Int. J. Bioinform. Res. Appl. Pub Date : 2020-02-02 DOI: 10.1504/ijbra.2020.10026538
Ashraf Hendam, A. Al-Sadek, H. Hefny
{"title":"In silico deleterious prediction of nonsynonymous single nucleotide polymorphisms in Neurexin1 gene for mental disorders","authors":"Ashraf Hendam, A. Al-Sadek, H. Hefny","doi":"10.1504/ijbra.2020.10026538","DOIUrl":"https://doi.org/10.1504/ijbra.2020.10026538","url":null,"abstract":"Neurexin1 (NRXN1) gene is playing an important role in synaptic formation, plasticity and maturity. Studies have reported non-synonymous SNPs in NRXN1 in patient with mental disorders. The current work is applying computational tools on recoded NRXN1 SNPs in mental disorder patients. The aim of the work is to identify deleterious SNPs, determine damaged protein features (function, stability) and recognise potential protein regions for future research. The effect on protein function is predicted by PROVEAN, SIFT and PolyPhen-2 while protein stability is predicted by MUpro and I-Mutant2.0. Prediction results have identified 2 SNPs to be deleterious by all tools. Higher deleterious results in the stability tools with the percentages of 72%, 78% than the function tools with 25%, 41% and 47%. Agreement percentage of deleterious prediction between stability tools was 56% while 12.5% in the function tools. The identified regions of NRXN1 for future research are SP and LNS4.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133907034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Identification of novel flowering genes using RNA-Seq pipeline employing combinatorial approach in Arabidopsis thaliana time-series apical shoot meristem data 利用RNA-Seq管道组合方法在拟南芥时间序列顶端分生组织数据中鉴定新的开花基因
Int. J. Bioinform. Res. Appl. Pub Date : 2020-02-02 DOI: 10.1504/ijbra.2020.10026539
Sumukh Deshpande, A. James, C. Franklin, Lindsey J. Leach, Jianhua Yang
{"title":"Identification of novel flowering genes using RNA-Seq pipeline employing combinatorial approach in Arabidopsis thaliana time-series apical shoot meristem data","authors":"Sumukh Deshpande, A. James, C. Franklin, Lindsey J. Leach, Jianhua Yang","doi":"10.1504/ijbra.2020.10026539","DOIUrl":"https://doi.org/10.1504/ijbra.2020.10026539","url":null,"abstract":"Floral transition is a crucial event in the reproductive cycle of a flowering plant during which many genes are expressed that govern the transition phase. Identification of additional genes connected to flowering genes is vital since they may regulate flowering genes and vice versa. Through our study, expression values of additional genes have been found similar to flowering genes FLC and LFY in the transition phase. The presented approach plays a crucial role in this discovery. An RNA-Seq computational pipeline was developed for identification of novel genes involved in floral transition from A. thaliana apical shoot meristem time-series data. By intersecting differentially expressed genes (DEGs) from Cuffdiff, DEseq and edgeR, we identified 30 genes as principle regulators in the transition phase. Additionally, expression profiles of highly connected genes from network analysis revealed 76 genes with non-functional association and high correlation to FLC and LFY suggesting their potential role in floral regulation.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127623392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Statistical analysis of the in silico binding affinity of P-glycoprotein and its substrates with their experimentally known parameters to demonstrate a cost-effective approach for screening, ranking and possible prediction of potential substrates 统计分析p -糖蛋白及其底物的硅结合亲和力及其实验已知参数，以证明筛选，排序和可能预测潜在底物的成本效益方法
Int. J. Bioinform. Res. Appl. Pub Date : 2019-11-25 DOI: 10.1504/ijbra.2019.10025474
A. Cleave, P. Suresh
{"title":"Statistical analysis of the in silico binding affinity of P-glycoprotein and its substrates with their experimentally known parameters to demonstrate a cost-effective approach for screening, ranking and possible prediction of potential substrates","authors":"A. Cleave, P. Suresh","doi":"10.1504/ijbra.2019.10025474","DOIUrl":"https://doi.org/10.1504/ijbra.2019.10025474","url":null,"abstract":"Over-expression of P-glycoprotein (P-gp) has been reported as a cause of multi-drug resistance in cancers and other diseases. Transport assays, which are generally used to find out the specificity of a compound to be effluxed, have always been time consuming, resource-intensive and expensive and thus, have inherent limitations to easily predict a compound's specificity. Hence, there is a clear-cut, unmet need to develop cost-effective methods for screening, identification and ranking of P-gp substrates. All compounds (23 substrates and 3 non-substrates) were docked to two homology modelled human P-gp conformations. The in silico binding affinities, obtained for all substrates, were checked for correlation with their experimentally determined efflux ratios, LogP values and number of hydrogen bond acceptors they possess. Docking results showed that all compounds demonstrated differences in relative binding affinity. Experimentally-derived efflux ratio obtained for 19 substrates from literature, for the first time showed a significant, Spearman correlation with binding energies to outward-facing conformation. Thus, it can be said that binding energies obtained from docking studies can possibly have significant potential in identifying the specificity and ranking P-gp substrates. This approach provides a sound foundation to strengthen the relationship of in silico binding energies with other experimentally defined physico-chemical parameters and can also be part of an iterative process to identify and develop a potential, validatable solution.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115474051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Detection of postural balance degradation using fuzzy neural network 基于模糊神经网络的姿态平衡退化检测
Int. J. Bioinform. Res. Appl. Pub Date : 2019-11-25 DOI: 10.1504/ijbra.2019.10025477
N. Singh
{"title":"Detection of postural balance degradation using fuzzy neural network","authors":"N. Singh","doi":"10.1504/ijbra.2019.10025477","DOIUrl":"https://doi.org/10.1504/ijbra.2019.10025477","url":null,"abstract":"Postural balance is often studied in order to understand the effect of sensory degradation with age. The aim of this study is to analyse the static and dynamic stabilogram signals to determine different features, which can be used to detect a degradation in equilibrium using the self-adaptive neurofuzzy inference systems (SANFIS). The main features are critical point interval (CPI), autoregressive moving average (ARMA) and area of a curve under the slope (Z-Area) that are identified from the stabilogram signals. The determined features of the stabilogram signals are used to detect and predict the degradation in postural balance using the fuzzy neural network. The selected features are randomly selected for training and testing during the classification and prediction in postural balance, where we have achieved average 95.3% accuracy of the result of classification and prediction of the degradation in equilibrium in 10 trials.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126717872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effect of single amino acid mutations on C-terminal domain of breast cancer susceptible protein 1 单氨基酸突变对乳腺癌易感蛋白c末端结构域的影响
Int. J. Bioinform. Res. Appl. Pub Date : 2019-11-25 DOI: 10.1504/ijbra.2019.10025475
Satish Kumar, Lingaraja Jena, Maheswata Sahoo, Kanchan Mohod, S. Daf, A. Varma
{"title":"Effect of single amino acid mutations on C-terminal domain of breast cancer susceptible protein 1","authors":"Satish Kumar, Lingaraja Jena, Maheswata Sahoo, Kanchan Mohod, S. Daf, A. Varma","doi":"10.1504/ijbra.2019.10025475","DOIUrl":"https://doi.org/10.1504/ijbra.2019.10025475","url":null,"abstract":"The most commonly diagnosed cancer in women is the breast cancer. Around 5-10% of breast cancer cases are hereditary, mainly due to the mutation in the breast cancer susceptible Breast Cancer 1 (BRCA1) and Breast Cancer 2 (BRCA2) tumour-suppressor genes. More than hundreds mutations are documented in BRCA1 C-terminal region (BRCT), mainly associated with repairing DNA damage and cell cycle control. In this study, we employed different mutation analysis system such as sorting intolerant from tolerant, MutPred, PON-P2, Meta-SNP, etc., to predict the pathological effects of 95 distinct miss sense mutation on BRCT domain. Out of which, 37 mutations were predicted to be deleterious by all mutation analysis systems affecting the protein stability and its normal function leading to causing cancer. The computational approach for finding out the impact of mutation on BRCA protein may provide a way in early detection and therapy in breast cancer patients.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131335052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Graph pruning based approach for inferring disease causing genes and associated pathways 基于图修剪的方法推断致病基因和相关途径
Int. J. Bioinform. Res. Appl. Pub Date : 2019-11-25 DOI: 10.1504/ijbra.2019.10025478
Jeethu V. Devasia, P. Chandran
{"title":"Graph pruning based approach for inferring disease causing genes and associated pathways","authors":"Jeethu V. Devasia, P. Chandran","doi":"10.1504/ijbra.2019.10025478","DOIUrl":"https://doi.org/10.1504/ijbra.2019.10025478","url":null,"abstract":"The problem of inferring disease causing genes and dysregulated pathways has obtained a vital position in computational biology research. But, the huge size of the biological network makes this process computationally challenging. Here, we tackle the problem of inferring disease causing genes and associated pathways using graph pruning techniques which focus on the improvement in accuracy of results in reasonable execution time and fetching more causal genes and their pathways. Experimentation of the proposed approach and the reported approaches in literature was done on real biological data. More efficient results in terms of accuracy and execution time based on benchmark datasets were obtained as its outcome. If the function of the newly identified genes/pathways in the disease states could be validated biologically, for any unknown influences in the disease development, it would significantly affect our effort to design new drug targets and defeat the diseases.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133194117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Long non-coding RNAs in animal genomes: challenges and promises 动物基因组中的长链非编码rna:挑战与前景
Int. J. Bioinform. Res. Appl. Pub Date : 2019-11-25 DOI: 10.1504/ijbra.2019.10025476
L. Fang, Prashanth Suravajhala
{"title":"Long non-coding RNAs in animal genomes: challenges and promises","authors":"L. Fang, Prashanth Suravajhala","doi":"10.1504/ijbra.2019.10025476","DOIUrl":"https://doi.org/10.1504/ijbra.2019.10025476","url":null,"abstract":"Majority of the eukaryotic genes do not code for proteins, i.e., there are regions without coding potential. If they do not code, it was earlier supposed to be of disinterest as they wouldn't be associated with any disease. However, the last decade has seen advances in the field with certain (non-coding) RNA molecules transcribed; regulate expression of genes and further known to affect the transcription and cell cycle of organism. A class of such non-coding RNAs identified during the last decade is long non-coding RNAs (lncRNA) that are known to play a role in wide variety of diseases. We outline a few challenges and promises of lncRNAs specific to animal/livestock genomes that we could exploit in identifying their role in various diseases. For brevity, we have considered bovine/clinical mastitis to show an example.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"75 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116598316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational study to understand mechanism of isoniazid drug resistance caused by mutation (R268H) in NADH dehydrogenase of Mycobacterium tuberculosis 计算研究结核分枝杆菌NADH脱氢酶突变(R268H)致异烟肼耐药机制
Int. J. Bioinform. Res. Appl. Pub Date : 2019-07-07 DOI: 10.1504/IJBRA.2019.101207
Lingaraja Jena, Shraddha Deshmukh, T. Nayak, G. Wankhade, B. Harinath
{"title":"Computational study to understand mechanism of isoniazid drug resistance caused by mutation (R268H) in NADH dehydrogenase of Mycobacterium tuberculosis","authors":"Lingaraja Jena, Shraddha Deshmukh, T. Nayak, G. Wankhade, B. Harinath","doi":"10.1504/IJBRA.2019.101207","DOIUrl":"https://doi.org/10.1504/IJBRA.2019.101207","url":null,"abstract":"NADH dehydrogenase (Ndh) of Mycobacterium tuberculosis is essential for conversion of NADH to NAD+ in the presence of FMN. An increased NADH/NAD+ ratio was reported due to mutation (R268H) in Ndh, causing INH resistance. To study the effect of this mutation on Ndh, molecular dynamics (MD) simulation analysis was performed for both wild and mutant models independently as well as for docked complexes (Ndh-NADH and Ndh-FMN). Simulation study showed that mutation (R268H) affected the secondary structure of the enzyme giving extra stability to the mutant model R268H as observed in the root mean square deviation (RMSD) plot. Furthermore, it was observed that both wild-type and mutant models of Ndh were quite stable in complex with NADH but in case of FMN, the Ndh mutant appears to be more unstable and might be the reason for decreasing NAD+ concentrations thus hindering INH-NAD adduct formation resulting in isoniazid resistance.","PeriodicalId":434900,"journal":{"name":"Int. J. Bioinform. Res. Appl.","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123953234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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